Here's a quick run-down on my system -- 3 amps (in-boat, tower, sub.) Up until yesterday they all worked without problem. Deck has 3-preouts. All RCA connections have been checked and seem good. I've also tried swapping RCA sources between the amps and it doesn't seem to have any effect.

If I turn the volume up more than 50% on the deck, the tower speakers start to almost oscillate/pan back and forth really quickly between right channel and left channel. The sub amp cuts out but seems to randomly "hit" or "pop" in a really weird way. The amps stay lit up correctly and I don't see any protection or clipping lights coming on. All fuses are also good.

If I disconnect the RCAs to the sub-amp, the exact same "hit/pop" continues... so it doesn't seem like it's related to the source.

If I unplug the tower speakers, everything works as it should (although the tower speakers obviously don't work.)

The tower speakers are being pushed by a PPI 4-channel amp that is being run in bridged stereo mode. Each "channel" is pushing one side of the tower. If I disconnect either channel, I still have the problem. This leads me to believe that the problem is not with the tower wiring or the speakers themselves.

All wiring is 00-gauge to a distribution block and then 2 channel to the amps. Plenty of 12v power. Have visually inspected all of the connections and wiring is flexible and seems to be in good shape. What next??

Okay, so you have two separate amplifiers behaving badly at the same time. Is it possible that both amplifiers have problematic issues with wiring or speakers after the amplifier? Maybe. But what do they have in common? The source electronics and the voltage.
First, substitute another source like an ipod direct....although the ipod may not have enough output voltage to trigger the problem....so try the ipod headphone out jack. Or try another substitiute CD player, any other player.
Next, and most important, measure the voltage across the amplifier primary terminals when the problem occurs, withOUT the boat running, and NOT at the battery terminals.
Something should be revealed.
This is the time of year when worn out batteries begin to surface as well as bad connections/terminations from a summer of shock and vibration.
Don't forget about exposure to water. A wet source unit could behave this way.

I agree with David. Take a voltage reading at the amps with the boat off as well as engine running. And if possible to induce the problem, take a reading when its happening. This is the best way to truly rule out a low voltage

Thanks, guys! At least I have some direction.... I don't believe it's the source because the sub amp misbehaves even with the RCAs disconnected! Easy to check, though....

Running a 3-bank stereo battery setup. Batteries are all under 24 months old and are left on a maintainer at all times. Dash gauge is showing 12v with the engine off and 14.4v when the engine is running. Problem persists whether boat is running or not. I know this doesn't rule out the wiring and probably the most likely place. I'll run some tests and report back! Thanks!

Well tightened/checked all my grounds and made sure batteries had a few days to charge and problems have gone away. Didn't get to test it for too long but was out for a couple of hours yesterday and didn't have any issues. Fingers crossed!